Backupninja has a MySQL backup feature, which dumps each database to a separate file. To restore, each database has to be created manually and each file needs to be imported. This backupninja action dumps all databases and their CREATE statements into a single file and backs it up:
mysqldump -u backup -p[passwd], --all-databases > /var/backups/mysql/all-databases.sql
gzip -f /var/backups/mysql/all-databases.sql